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PXD053582

PXD053582 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProtein misfolding involving entanglements provides a structural explanation for the origin of stretched-exponential refolding kinetics
DescriptionStretched-exponential protein refolding kinetics, first observed decades ago, were attributed to a nonnative ensemble of structures with parallel, non-interconverting folding pathways. However, the structural origin of the large energy barriers preventing interconversion between these folding pathways is unknown. Here, we combine simulations with limited proteolysis (LiP) and cross-linking (XL) mass spectrometry (MS) to study the protein phosphoglycerate kinase (PGK). Simulations recapitulate its stretched-exponential folding kinetics and reveal that misfolded states involving changes of entanglement underlie this behavior: either formation of a nonnative, noncovalent lasso entanglement or failure to form a native entanglement. These misfolded states act as kinetic traps, requiring extensive unfolding to escape, which results in a distribution of free energy barriers and pathway partitioning. Using LiP-MS and XL-MS, we propose heterogeneous structural ensembles consistent with these data that represent the potential long-lived misfolded states PGK populates. This structural and energetic heterogeneity creates a hierarchy of refolding timescales, explaining stretched-exponential kinetics.
HostingRepositoryPRIDE
AnnounceDate2025-03-18
AnnouncementXMLSubmission_2025-03-17_18:33:22.130.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterYingzi Xia
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListcarbamoylated residue; acetylated residue; monohydroxylated residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-07-02 17:23:27ID requested
12025-03-17 18:33:22announced
Publication List
Jiang Y, Xia Y, Sitarik I, Sharma P, Song H, Fried SD, O'Brien EP, Protein misfolding involving entanglements providesa structural explanation for the origin of stretched-exponential refolding kinetics. Sci Adv, 11(11):eads7379(2025) [pubmed]
10.1126/sciadv.ads7379;
Keyword List
submitter keyword: folding, crosslinking mass spectrometry, stretched-exponential kinetics
Contact List
Stephen Fried
contact affiliationAssistant Professor, Department of Chemistry Assistant Professor, Thomas C. Jenkins Department of Biophysics (by courtesy)
contact emailsdfried@jhu.edu
lab head
Yingzi Xia
contact affiliationJohns Hopkins University
contact emailyxia39@jhu.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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